<DIV>Hi Tom,</DIV>
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<DIV> Thanks so much ! You did surprize me indeed with Chimera capabilities that I wasn't aware of. I'll try your suggestions very soon.</DIV>
<DIV> </DIV>
<DIV> Cheers,</DIV>
<DIV> </DIV>
<DIV> Boaz </DIV>
<DIV> </DIV>
<DIV>P.S. We have a Nature Chemical Biology paper coming up soon with some Chimera pictures in it (and in the supplementary online material). I'll send the pdf's once it's online. <BR><BR>----- Original Message -----<BR>From: Tom Goddard <goddard@cgl.ucsf.edu><BR>Date: Sunday, December 16, 2007 2:29<BR>Subject: Re: [Chimera-users] crystallographic symmops and lattice translationsin Chimera<BR>To: Boaz Shaanan <bshaanan@bgu.ac.il><BR>Cc: chimera-users@cgl.ucsf.edu<BR><BR>> Hi Boaz,<BR>> <BR>> Chimera can apply lattice translations in a variety of <BR>> ways, though <BR>> there isn't currently a simple flexible command for this. <BR>> The <BR>> Multiscale tool (menu Tools / Higher-Order Structure) can make a <BR>> 3 by 3 <BR>> by 3 array of unit cells, and you can drag to select and delete <BR>> unwanted <BR>> monomers. The Unit Cell tool (same menu) can translate the <BR>> unit cell <BR>> origin (values 0-1) and reposition all asym units to have their <BR>> centers <BR>> in the cell. That only allows translation by a fraction of <BR>> a unit <BR>> cell. The Crystal Coordinates script on the experimental <BR>> features web <BR>> page can write out PDB files for a block of unit cells. <BR>> That has to be <BR>> downloaded separately:<BR>> <BR>> <BR>> http://www.cgl.ucsf.edu/chimera/experimental/experimental.html<BR>> Another trick is you could open two copies of your PDB translate <BR>> one by <BR>> one unit cell length along x with a command line "move x 123.5" <BR>> then <BR>> apply the Unit Cell tool to both copies. You'd have to get <BR>> the unit <BR>> cell size in x by looking at the CRYST1 record in the PDB file.<BR>> <BR>> The Unit Cell tool has a button "Outline unit cell" that <BR>> displays an <BR>> outline box for the unit cell of a chosen PDB model.<BR>> <BR>> Tom<BR>> <BR>> </DIV><BR><BR>Boaz Shaanan, Ph.D.
<br>Dept. of Life Sciences
<br>Ben-Gurion University of the Negev
<br>Beer-Sheva 84105
<br>Israel
<br>Phone: 972-8-647-2220 ; Fax: 646-1710
<br>Skype: boaz.shaanan</BR></BR>